5XTV

Crystal Structure of Transketolase in complex with TPP intermediate V from Pichia Stipitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.931 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Mesomeric Effect of Thiazolium on non-Kekule Diradicals in Pichia stipitis Transketolase.

Hsu, N.S.Wang, Y.L.Lin, K.H.Chang, C.F.Lyu, S.Y.Hsu, L.J.Liu, Y.C.Chang, C.Y.Wu, C.J.Li, T.L.

(2018) Angew. Chem. Int. Ed. Engl. 57: 1802-1807

  • DOI: 10.1002/anie.201709799
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • It is theoretically plausible that thiazolium mesomerizes to congeners other than carbene in a low effective dielectric binding site; especially given the energetics and uneven electronegativity of carbene groups. However, such a phenomenon has never ...

    It is theoretically plausible that thiazolium mesomerizes to congeners other than carbene in a low effective dielectric binding site; especially given the energetics and uneven electronegativity of carbene groups. However, such a phenomenon has never been reported. Nine crystal structures of transketolase obtained from Pichia stipitis (TKps) are reported with subatomic resolution, where thiazolium displays an extraordinary ring-bending effect. The bent thiazolium congeners correlate with non-Kekulé diradicals because there is no gain or loss of electrons. In conjunction with biophysical and biochemical analyses, it is concluded that ring bending is a result of tautomerization of thiazolium with its non- Kekulé diradicals, exclusively in the binding site of TKps. The chemophysical properties of these thiazolium mesomers may account for the great variety of reactivities carried out by thiamine-diphosphate-containing (ThDP) enzymes. The stability of ThDP in living systems can be regulated by the levels of substrates, and hydration and dehydration, as well as diradical-mediated oxidative degradation.


    Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.,Department of Food Science, National (Taiwan) Ocean University, Keelung, 202, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transketolase
A
697Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545)Mutation(s): 0 
Gene Names: TKT (TKT1)
EC: 2.2.1.1
Find proteins for P34736 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545))
Go to Gene View: TKT
Go to UniProtKB:  P34736
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
8EF
Query on 8EF

Download SDF File 
Download CCD File 
A
2-[(5S)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate
C12 H20 N4 O7 P2 S
YBJKPSYOFQHZDJ-NSHDSACASA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.931 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.131 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 101.023α = 90.00
b = 184.583β = 90.00
c = 99.136γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release